Magnesium in PDB 3dyn: Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited)

All present enzymatic activity of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited):
3.1.4.35;

The structure of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited), PDB code: 3dyn was solved by S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.857, 103.857, 270.118, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.3

The structure of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) (pdb code 3dyn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited), PDB code: 3dyn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:36.3 occ:1.00 O A:HOH1003 2.2 28.1 1.0 O A:HOH1002 2.3 27.5 1.0 OD1 A:ASP293 2.3 32.3 1.0 O A:HOH1000 2.3 27.0 1.0 O A:HOH1004 2.4 29.0 1.0 CG A:ASP293 3.3 32.4 1.0 O1A A:PCG903 3.3 51.7 1.0 OD2 A:ASP293 3.6 32.4 1.0 NE2 A:HIS325 4.0 28.6 1.0 ZN A:ZN901 4.0 31.9 1.0 O A:HIS292 4.1 31.9 1.0 OE2 A:GLU322 4.1 39.3 1.0 OG1 A:THR363 4.1 34.1 1.0 CD2 A:HIS325 4.2 30.0 1.0 CD2 A:HIS292 4.2 29.7 1.0 O2A A:PCG903 4.3 50.5 1.0 O A:HOH1001 4.3 41.9 1.0 O A:HOH1064 4.3 43.2 1.0 PA A:PCG903 4.3 48.2 1.0 OD2 A:ASP402 4.4 34.0 1.0 CD2 A:HIS296 4.6 31.5 1.0 CB A:ASP293 4.6 30.1 1.0 NE2 A:HIS292 4.6 30.1 1.0 O5' A:PCG903 4.7 49.1 1.0 CG A:GLU322 4.7 30.8 1.0 CB A:THR363 4.7 34.0 1.0 O A:THR363 4.8 32.7 1.0 CD A:GLU322 4.8 37.9 1.0 CA A:ASP293 4.8 30.7 1.0 O A:HOH1196 4.9 50.6 1.0 CD2 A:HIS252 4.9 32.6 1.0 NE2 A:HIS252 4.9 36.6 1.0 NE2 A:HIS296 4.9 30.7 1.0 C A:HIS292 4.9 30.1 1.0

Magnesium binding site 2 out of 2 in the Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphodiestrase 9 in Complex with Cgmp (Zn Inhibited) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:40.5 occ:1.00 O B:HOH905 2.3 30.1 1.0 O B:HOH907 2.3 35.4 1.0 OD1 B:ASP293 2.3 33.4 1.0 O2A B:PCG900 2.4 36.5 0.5 O B:HOH904 2.4 32.0 1.0 O B:HOH906 2.4 30.9 1.0 CG B:ASP293 3.3 31.7 1.0 PA B:PCG900 3.4 50.5 0.5 OD2 B:ASP293 3.6 34.9 1.0 O5' B:PCG900 3.7 42.7 0.5 NE2 B:HIS325 3.9 28.4 1.0 O1A B:PCG900 3.9 35.6 0.5 OE2 B:GLU322 4.0 40.0 1.0 O B:HOH994 4.0 38.4 1.0 ZN B:ZN901 4.1 34.2 1.0 CD2 B:HIS325 4.2 30.3 1.0 O B:HIS292 4.3 32.2 1.0 CD2 B:HIS296 4.4 30.4 1.0 CD2 B:HIS292 4.4 30.1 1.0 OG1 B:THR363 4.4 33.2 1.0 OD2 B:ASP402 4.6 33.1 1.0 NE2 B:HIS296 4.6 30.6 1.0 CB B:ASP293 4.6 31.4 1.0 NE2 B:HIS252 4.7 36.5 1.0 CD2 B:HIS252 4.7 32.2 1.0 CG B:GLU322 4.8 30.9 1.0 CD B:GLU322 4.8 38.7 1.0 O B:THR363 4.8 33.3 1.0 NE2 B:HIS292 4.9 30.2 1.0 O B:HOH1049 4.9 44.9 1.0 CB B:THR363 4.9 34.5 1.0 CA B:ASP293 4.9 30.6 1.0 O3' B:PCG900 4.9 44.6 0.5

S.Liu, M.N.Mansour, K.S.Dillman, J.R.Perez, D.E.Danley, P.A.Aeed, S.P.Simons, P.K.Lemotte, F.S.Menniti. Structural Basis For the Catalytic Mechanism of Human Phosphodiesterase 9. Proc.Natl.Acad.Sci.Usa V. 105 13309 2008.
ISSN: ISSN 0027-8424
PubMed: 18757755
DOI: 10.1073/PNAS.0708850105